In mass spectrometry, peptide ions are often fragmented prior to mass analysis. A relatively new method of peptide fragmentation entails reaction of peptide cations and reagent anions in quadrupole ion traps, in particular, in linear ion traps (LIT) based on a quadruple set of rod electrodes, which utilize radio-frequency (RF) fields for ion confinement. The technical literature typically refers to an ion-ion fragmentation reaction as Electron-Transfer Dissociation (ETD), in which electron transfer is assumed to be central to the reaction process.
In principal, as described by Liang, Hager and McLuckey, Analytical Chemistry, Vol. 79, pages 3363-3370 (2007), four methods provide peptide ion ETD reactions in a LIT. Three of these methods entail allowing cations and/or anions to pass through the LIT, i.e., only cations or anions, or neither, are confined in the LIT. These three methods use a DC potential barrier for axial confinement of ions of a single polarity (where “axial” is a conventional reference to the lengthwise direction of a LIT.) The fourth method simultaneously confines ions of opposite polarities (i.e., cations and anions) along the axial direction, through use of RF pseudopotential barriers or application, to the quadrupole rod set, of unbalanced RF fields. An axial pseudopotential barrier is formed, for example, with application, to containment lenses at the axial ends of the LIT, of RF oscillating potentials.
Optimal ion flow control is difficult to achieve with single-polarity confinement because the DC potential barrier, used for axial confinement of ions of a single polarity, acts as an accelerating potential for the opposite-polarity ions flowing through the LIT. Thus, the kinetic energy difference between the flowing ions and the confined ions may be too high for some ion-ion reactions to favorably occur; ETD researchers believe that the ion-ion reaction rate is inversely proportional to the cube of the relative velocity between the ions. Thus, mutual storage of peptide cations and reagent anions is expected to provide the lowest relative ion velocities, for more efficient dissociation.
Mutual confinement, however, as indicated, above, typically requires more complex use of RF voltages. Moreover, the barrier height of an RF-generated pseudopotential barrier is a function of the mass-to-charge ratio of the ions being stored, thus restricting the mass range of analyte or reagent ions that can be mutually confined for ion-ion reactions.
As an alternative to reliance on RF fields for mutual confinement, two separate quadrupole rod sets, i.e., two adjacent LITs, are used to separately store cations and anions in the two adjacent LITs, prior to allowing ions from one LIT to flow through the other LIT. Such an approach to mutual confinement, however, increases the complexity and cost of a fragmentation device.